Plectix Blog

Lessons from the Cutting Edge of Technology

By Joshua Havumaki

My over two years at Plectix come to a close this week. Below are my experiences working in an interdisciplinary start-up company.

I first joined as an intern in summer 2007. Plectix was a rapidly developing company yet to be fully established. During the summer, I was the only biologist amongst mostly computer science academics. This presented an exciting challenge for me. Since I had little quantitative experience and absolutely no exposure to modeling or computer science, it was an unparalleled opportunity to learn.  When I returned to Plectix full-time in early 2008, the team expanded as we began designing our flagship product, Cellucidate.

Aside from designing Cellucidate, the bulk of my time here has involved collating and modeling the large and complex EGFR pathway. Due to the fact that this was a new space for me, a significant portion of my time was spent learning and understanding the methods and nuances of modeling. This has also been a learn-as-you-go type of experience filled with many things that could not have been anticipated. Here are a few key lessons I’ve learned from working on the project.

First, the limitations of experimental and modeling methods should always be thoroughly discussed to ensure that experimental data can effectively complement the modeling work. Quantitative data can be deceptive, contextual and not appropriate for modeling. Second, when experts in different fields communicate it is quite possible to interpret terminology differently. This can result in a completely incorrect understanding of the technology or content.  Finally, being fully aware of the feasibility of large projects is essential. For instance, manually tweaking rates on my large model at first seemed quite effective for fitting the model to data, but eventually turned out to be nearly impossible.

Overall, this invaluable experience has exposed me to systems biology from both the academic and commercial sectors. I won't soon forget many of the lessons I've learned here and I know that they will prime me well for a future career in systems biology.

Biophysics in Boston

By Isha Antani

 

Biophysics is an interdisciplinary field that looks at biology from the lens of physic fundamentals. Relying heavily on quantitative means and mathematical theorems, the field adds an an extra dimension to the study of biological principles. Due to its quantitative nature, biophysics primarily focuses on networks and communications found in both intra- and extra-cellular space.

 

Recently the Council for Systems Biology held an all-day session on Biophysics as part of its annual Cell, Circuits, and Computation meeting. Many of the talks held my interest, but one was a pure standout - that of Dr. Jennifer Ross from University of Massachusetts on the complexity in cytoskeletal networks. Dr. Ross gave a dynamic, vivid presentation on the "walking" mechanisms of the kinesin and dynein motor proteins and the reason for their specific localizations in the cell. It wasn't just the nature of the talk but the manner in which the talk was delivered that captivated the audience. Other talks in the conference covered areas from nuclear pores to cutting-edge microarray technology. Overall, the conference presented a fair insight into the interesting work being done in biophysics.

Shift to Vaccines

By Vy Hoang

Due to high failure rates in clinical drug trials, generic drug competition and loss of patent protection for blockbuster drugs in the upcoming years, big pharmaceutical companies are shifting their research attention towards creating new vaccines to prevent a range of illnesses and diseases. During the booming years of drug discovery, vaccines were overlooked by the pharmaceutical industry, but now vaccines are back in the spotlight because of a growing global market.

Various factors have renewed this interest in vaccines, such as rising prices and an increased demand for vaccines. In general, vaccines are a safe investment because they work. Since 1900, mass vaccination along with improved sanitation has increased the life expectancy from 47 to 77 years in wealthy countries. Just one or several doses of a vaccine can produce a lifelong protection against infections, which in the long run is very cost-effective to the consumer and insurer. This leads to the reason why vaccines are increasing in demand.

With the growing populations and economies, more money is being spent on healthcare. Developing countries such as China and India, which are emerging healthcare consumers, are increasingly spending money on vaccines in order to prevent diseases and save money in the long term. Nonprofit organizations, as well, are buying lots of vaccines to distribute among underdeveloped countries, thus escalating demand. Additionally, governments are willing to buy and stockpile large amounts of vaccines for naturally occurring diseases and against bioterrorism agents. For example, in the recent pandemic H1N1 influenza, governments worldwide spent several billions of dollars for the H1N1 vaccine.

Of course, another incentive for pharmas to invest in vaccines is the rising price of vaccines. In the 1980s, standard vaccines (measles, mumps, rubella) for children were around $7 a dose but now the price has shot up to $28. Even common vaccines (tetanus and pertussis) jumped ten-fold, from $1.60 to $16.64. Several pharmas, including Novartis, Sanofi-Aventis, and Merck, reported that many years ago only 3-5% of their revenue came from vaccines, compared to now, where it is about 11-15%.

All of these factors are good news for the big pharma companies who are struggling with drug discovery. These companies are currently working on new vaccines that will tackle diseases such as malaria, tuberculosis, and AIDS. Thus, the best news is for us, the consumers who are benefiting from their success.

Bringing Minds Together

By Isha Antani

Yes, many of us are aware of the issues that the current pharmaceutical industry is facing. It’s a well-known fact that more money being pumped into the drug discovery process is resulting in less drug discovery. This is due to high failure rates of potential drug candidates either in Phase I (safety) or Phase 2 (efficacy) of the pipeline. 

Academia, while known to have a good target discovery rate, is weak in the area of drug discovery and often has to spend a good amount of time seeking financial means to support its work. Additionally, while pharmaceuticals spend large sums on high-risk drugs with blockbuster potential, academia is more attuned to researching rare cases and is often funded by foundations set up for these specific cases. Both pharma and academia could use a bit of help from one another. And, slowly, both are.

Up until the 1980s, there was a huge barrier to get pharmaceuticals to invest in targets discovered in academic labs. Academic labs that had been funded by the government were not allowed to patent their efforts. Therefore, pharmaceuticals didn’t really have the incentive to go after a drug that any other company could also potentially develop. However, in the 1980s the Bayh-Dole act was passed which allowed patents to be placed on federally funded research projects, leading to a much better technology transfer between the two arms. However, true collaboration was still lacking. 

Now, due to the current dismal state of drug pipelines, the two sectors have been coming together for various initiatives with hopes that better targets generated by academia will lead to better (and cheaper) drug development. AstraZeneca, for example, has collaborated with Columbia University to understand the area of metabolic diseases while Pfizer, a big believer in academia-industry collaboration, has multiple projects with academia. The collaboration makes sense and in a way, there are incentives for both parties involved—the academic labs, who carry the focused expertise, retain the intellectual property rights on their discovery while the pharmas, who are profit-making companies, save money in the discovery process and get the right into developing the process and marketing the discovered target in their preferred manner. It’s a win-win situation for both parties and for the greater public, who gets to see effective, cheaper drugs on the market at a faster rate.

Second Annual Molecular Programming Project Workshop

By Traci Freed

The Second Annual Molecular Programming Project Workshop is being held this weekend in Oxnard, CA.  Walter Fontana will be presenting a talk on January 10th at 10 am.  If you are attending this conference, be sure to go to Walter's talk to learn more about Cellucidate, our web-based, collaborative workspace for cell biology.  We hope to see you there!